Arms deal inquiry chairperson Judge Willie Seriti on Monday challenged lawyer Norman Moabi to provide proof the commission had a "second agenda".
"If Mr [Norman] Moabi had proof of the second agenda that he alleges he should simply have produced it," Seriti said in a statement.
"He cannot rely on his misplaced perceptions."
Moabi, a lawyer and former acting judge from Pretoria, alleged in a letter, which was leaked to Beeld newspaper, that the commission into the arms deal was not being transparent and concealing a "second agenda".
Moabi wrote in the letter, addressed to Seriti, that he was resigning because of interference and because he had lost faith in the commission's work.
According to Moabi, Seriti ruled the commission with an iron fist and facts were manipulated or withheld from commissioners. Contributions from commissioners who did not pursue the "second agenda" were frequently ignored.
In the Mail&Guardian on Friday, Moabi challenged Seriti to take a lie detector test, saying he would also take one. This was after Seriti denied Moabi's allegations. Seriti on Monday said he did not intend on engaging in a public spat with Moabi.
However, he said Moabi's allegations against the evidence leaders were "unbelievable and appalling".
"I note that he also throws aspersions on the bona fides of the evidence leaders who, on their own initiative, issued a media statement stating their views on the alleged second agenda.
"He even disputes that consultations and planning sessions with them, where their inputs were sought, ever took place."
Seriti said the commission would not respond to any further media questions relating to Moabi's allegations.
"I wish to appeal to the media and the public at large to give the commission space to focus on preparations for the upcoming public hearings," he said.
Hearings were expected to start in March.
In October 2011, President Jacob Zuma announced that Supreme Court of Appeal Judge Seriti would chair the three-man commission of inquiry, assisted by judges Hendrick Musi and Francis Legodi.
Initially, Judge Willem van der Merwe — the same judge who acquitted Zuma on a rape charge — was appointed to help Seriti, alongside Legodi.
However, in December 2011, the Presidency said Van der Merwe had indicated he would not be able to serve on the commission, for personal reasons.
Zuma then appointed Free State High Court Judge President Musi to replace Van der Merwe.
In May, commission secretary Mvuseni Ngubane was found dead on the back seat of his car in Pinetown, KwaZulu-Natal. Police said a suicide note was found near the body, but that parts of it were illegible because of blood stains. It was thus not clear why he committed suicide.
As secretary of the commission he would have been responsible for managing its budget and ensuring it had administrative support.
The multi-million rand arms deal has dogged South Africa's politics since it was signed in 1999, after then Pan Africanist Congress MP Patricia de Lille raised allegations of corruption in Parliament.
Zuma was himself charged with corruption after his financial adviser Schabir Shaik, who had a tender to supply part of the requirements, was found to have facilitated a bribe for him from a French arms company.
The charges against Zuma were later dropped.